Starting phenix.real_space_refine
on Tue Feb  3 15:34:41 2026 by dcliebschner
===============================================================================

Processing files:
-------------------------------------------------------------------------------

  Found model, /net/cci-nas-00/data/ceres_data/9oq0_70732/02_2026/9oq0_70732.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9oq0_70732/02_2026/9oq0_70732.map

Processing PHIL parameters:
-------------------------------------------------------------------------------

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.67
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9oq0_70732/02_2026/9oq0_70732.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9oq0_70732/02_2026/9oq0_70732.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9oq0_70732/02_2026/9oq0_70732.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9oq0_70732/02_2026/9oq0_70732.cif"
  }
  resolution = 3.67
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.004 sd=   0.089
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      38      5.16       5
     C    2888      2.51       5
     N     682      2.21       5
     O     721      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 4329
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 2183
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 278, 2183
          Classifications: {'peptide': 278}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 17, 'TRANS': 260}
    Chain: "B"
      Number of atoms: 2146
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 275, 2146
          Classifications: {'peptide': 275}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 16, 'TRANS': 258}
  Time building chain proxies: 0.78, per 1000 atoms: 0.18
  Number of scatterers: 4329
  At special positions: 0
  Unit cell: (69.9336, 82.6488, 93.7746, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      38     16.00
     O     721      8.00
     N     682      7.00
     C    2888      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 630 " - pdb=" SG  CYS A 720 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 638 " - pdb=" SG  CYS B 727 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.23
  Conformation dependent library (CDL) restraints added in 105.0 milliseconds
  

  1098 Ramachandran restraints generated.
    549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1050

  Finding SS restraints...
    Secondary structure from input PDB file:
      27 helices and 2 sheets defined
      82.1% alpha, 3.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.08
  Creating SS restraints...
    Processing helix  chain 'A' and resid 563 through 588
    Processing helix  chain 'A' and resid 593 through 600
      removed outlier: 3.950A  pdb=" N   GLY A 600 " --> pdb=" O   VAL A 596 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 601 through 615
    Processing helix  chain 'A' and resid 616 through 622
    Processing helix  chain 'A' and resid 626 through 635
      removed outlier: 4.129A  pdb=" N   CYS A 632 " --> pdb=" O   SER A 628 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 635 through 656
      removed outlier: 3.655A  pdb=" N   CYS A 644 " --> pdb=" O   CYS A 640 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 657 through 665
      removed outlier: 3.610A  pdb=" N   MET A 661 " --> pdb=" O   CYS A 657 " (cutoff:3.500A)
      removed outlier: 3.983A  pdb=" N   ALA A 662 " --> pdb=" O   ALA A 658 " (cutoff:3.500A)
      removed outlier: 4.021A  pdb=" N   SER A 663 " --> pdb=" O   PHE A 659 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 665 through 673
      removed outlier: 4.762A  pdb=" N   TYR A 671 " --> pdb=" O   ARG A 667 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 678 through 701
      removed outlier: 4.213A  pdb=" N   ILE A 695 " --> pdb=" O   VAL A 691 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 723 through 749
      removed outlier: 3.753A  pdb=" N   PHE A 730 " --> pdb=" O   ASN A 726 " (cutoff:3.500A)
      removed outlier: 3.794A  pdb=" N   ASN A 731 " --> pdb=" O   SER A 727 " (cutoff:3.500A)
      removed outlier: 4.260A  pdb=" N   LEU A 734 " --> pdb=" O   PHE A 730 " (cutoff:3.500A)
      removed outlier: 3.823A  pdb=" N   ASP A 735 " --> pdb=" O   ASN A 731 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 753 through 783
      removed outlier: 6.076A  pdb=" N   ALA A 759 " --> pdb=" O   ASN A 755 " (cutoff:3.500A)
      removed outlier: 7.160A  pdb=" N   LYS A 760 " --> pdb=" O   TYR A 756 " (cutoff:3.500A)
      removed outlier: 4.548A  pdb=" N   PHE A 761 " --> pdb=" O   ASN A 757 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 787 through 816
      removed outlier: 3.644A  pdb=" N   TYR A 807 " --> pdb=" O   ILE A 803 " (cutoff:3.500A)
      Proline residue:  A 810  - end of helix
      removed outlier: 3.673A  pdb=" N   LEU A 816 " --> pdb=" O   CYS A 812 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 823 through 831
      removed outlier: 3.753A  pdb=" N   ASN A 828 " --> pdb=" O   ALA A 825 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 571 through 598
    Processing helix  chain 'B' and resid 601 through 607
    Processing helix  chain 'B' and resid 609 through 624
      removed outlier: 3.899A  pdb=" N   CYS B 613 " --> pdb=" O   GLY B 609 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 625 through 629
      removed outlier: 3.541A  pdb=" N   PHE B 629 " --> pdb=" O   VAL B 626 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 634 through 668
      removed outlier: 4.524A  pdb=" N   GLN B 642 " --> pdb=" O   CYS B 638 " (cutoff:3.500A)
      Proline residue:  B 643  - end of helix
      Proline residue:  B 648  - end of helix
      removed outlier: 4.810A  pdb=" N   THR B 655 " --> pdb=" O   GLY B 651 " (cutoff:3.500A)
      removed outlier: 3.794A  pdb=" N   LEU B 656 " --> pdb=" O   CYS B 652 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 670 through 682
      removed outlier: 4.331A  pdb=" N   TRP B 676 " --> pdb=" O   SER B 672 " (cutoff:3.500A)
      removed outlier: 3.956A  pdb=" N   SER B 679 " --> pdb=" O   ASN B 675 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 683 through 708
      removed outlier: 3.889A  pdb=" N   TRP B 687 " --> pdb=" O   GLY B 683 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 731 through 754
      removed outlier: 3.763A  pdb=" N   VAL B 738 " --> pdb=" O   SER B 734 " (cutoff:3.500A)
      removed outlier: 4.929A  pdb=" N   THR B 741 " --> pdb=" O   LEU B 737 " (cutoff:3.500A)
      removed outlier: 5.175A  pdb=" N   ASN B 742 " --> pdb=" O   VAL B 738 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 764 through 790
      removed outlier: 4.526A  pdb=" N   GLY B 768 " --> pdb=" O   ASN B 764 " (cutoff:3.500A)
      removed outlier: 3.740A  pdb=" N   LEU B 769 " --> pdb=" O   ARG B 765 " (cutoff:3.500A)
      removed outlier: 3.991A  pdb=" N   VAL B 784 " --> pdb=" O   TRP B 780 " (cutoff:3.500A)
      Proline residue:  B 785  - end of helix
    Processing helix  chain 'B' and resid 791 through 793
      No H-bonds generated for 'chain 'B' and resid 791 through 793'
    Processing helix  chain 'B' and resid 794 through 815
      removed outlier: 3.744A  pdb=" N   VAL B 798 " --> pdb=" O   TYR B 794 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   THR B 813 " --> pdb=" O   GLY B 809 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 815 through 825
      removed outlier: 3.548A  pdb=" N   VAL B 821 " --> pdb=" O   PRO B 817 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 826 through 829
    Processing helix  chain 'B' and resid 830 through 835
      removed outlier: 3.652A  pdb=" N   PHE B 834 " --> pdb=" O   THR B 830 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 555 through 557
      removed outlier: 6.203A  pdb=" N   GLN A 555 " --> pdb=" O   THR A 716 " (cutoff:3.500A)
      removed outlier: 7.092A  pdb=" N   VAL A 718 " --> pdb=" O   GLN A 555 " (cutoff:3.500A)
      removed outlier: 6.463A  pdb=" N   VAL A 557 " --> pdb=" O   VAL A 718 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 563 through 565
      removed outlier: 6.293A  pdb=" N   ARG B 563 " --> pdb=" O   VAL B 723 " (cutoff:3.500A)
      removed outlier: 7.226A  pdb=" N   GLU B 725 " --> pdb=" O   ARG B 563 " (cutoff:3.500A)
      removed outlier: 6.109A  pdb=" N   LYS B 565 " --> pdb=" O   GLU B 725 " (cutoff:3.500A)
      removed outlier: 8.453A  pdb=" N   CYS B 727 " --> pdb=" O   LYS B 565 " (cutoff:3.500A)

    312 hydrogen bonds defined for protein.
    909 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.43

  Time building geometry restraints manager: 0.31 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        1.21 -     1.34: 1273
        1.34 -     1.46: 1118
        1.46 -     1.59: 2013
        1.59 -     1.71: 0
        1.71 -     1.83: 54
  Bond restraints: 4458
  Sorted by residual:
  bond pdb=" N   SER B 601 "
       pdb=" CA  SER B 601 "
    ideal  model  delta    sigma   weight residual
    1.454  1.485 -0.032 1.14e-02 7.69e+03 7.66e+00
  bond pdb=" N   VAL B 604 "
       pdb=" CA  VAL B 604 "
    ideal  model  delta    sigma   weight residual
    1.461  1.493 -0.033 1.19e-02 7.06e+03 7.58e+00
  bond pdb=" N   VAL B 733 "
       pdb=" CA  VAL B 733 "
    ideal  model  delta    sigma   weight residual
    1.461  1.492 -0.031 1.17e-02 7.31e+03 6.94e+00
  bond pdb=" N   HIS B 597 "
       pdb=" CA  HIS B 597 "
    ideal  model  delta    sigma   weight residual
    1.459  1.489 -0.030 1.19e-02 7.06e+03 6.43e+00
  bond pdb=" N   ASP B 600 "
       pdb=" CA  ASP B 600 "
    ideal  model  delta    sigma   weight residual
    1.458  1.491 -0.034 1.33e-02 5.65e+03 6.43e+00
  ... (remaining 4453 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.48: 5789
        1.48 -     2.96: 250
        2.96 -     4.45: 55
        4.45 -     5.93: 6
        5.93 -     7.41: 3
  Bond angle restraints: 6103
  Sorted by residual:
  angle pdb=" N   ARG B 765 "
        pdb=" CA  ARG B 765 "
        pdb=" C   ARG B 765 "
      ideal   model   delta    sigma   weight residual
     111.69  117.42   -5.73 1.23e+00 6.61e-01 2.17e+01
  angle pdb=" C   ARG A 674 "
        pdb=" N   TYR A 675 "
        pdb=" CA  TYR A 675 "
      ideal   model   delta    sigma   weight residual
     121.54  128.95   -7.41 1.91e+00 2.74e-01 1.50e+01
  angle pdb=" N   LEU B 656 "
        pdb=" CA  LEU B 656 "
        pdb=" C   LEU B 656 "
      ideal   model   delta    sigma   weight residual
     111.28  107.33    3.95 1.09e+00 8.42e-01 1.32e+01
  angle pdb=" N   ILE B 740 "
        pdb=" CA  ILE B 740 "
        pdb=" C   ILE B 740 "
      ideal   model   delta    sigma   weight residual
     110.53  113.93   -3.40 9.40e-01 1.13e+00 1.31e+01
  angle pdb=" N   ALA B 660 "
        pdb=" CA  ALA B 660 "
        pdb=" C   ALA B 660 "
      ideal   model   delta    sigma   weight residual
     111.28  107.67    3.61 1.09e+00 8.42e-01 1.10e+01
  ... (remaining 6098 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.87: 2398
       15.87 -    31.74: 150
       31.74 -    47.61: 42
       47.61 -    63.49: 4
       63.49 -    79.36: 1
  Dihedral angle restraints: 2595
    sinusoidal: 973
      harmonic: 1622
  Sorted by residual:
  dihedral pdb=" CA  GLU B 666 "
           pdb=" C   GLU B 666 "
           pdb=" N   SER B 667 "
           pdb=" CA  SER B 667 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -157.63  -22.37     0      5.00e+00 4.00e-02 2.00e+01
  dihedral pdb=" CA  SER B 667 "
           pdb=" C   SER B 667 "
           pdb=" N   GLU B 668 "
           pdb=" CA  GLU B 668 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.85   19.15     0      5.00e+00 4.00e-02 1.47e+01
  dihedral pdb=" CA  ASP A 711 "
           pdb=" C   ASP A 711 "
           pdb=" N   ASP A 712 "
           pdb=" CA  ASP A 712 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.61   18.39     0      5.00e+00 4.00e-02 1.35e+01
  ... (remaining 2592 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.043: 563
       0.043 -    0.086: 124
       0.086 -    0.129: 35
       0.129 -    0.171: 5
       0.171 -    0.214: 1
  Chirality restraints: 728
  Sorted by residual:
  chirality pdb=" CA  VAL B 733 "
            pdb=" N   VAL B 733 "
            pdb=" C   VAL B 733 "
            pdb=" CB  VAL B 733 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.66   -0.21 2.00e-01 2.50e+01 1.15e+00
  chirality pdb=" CA  ILE A 643 "
            pdb=" N   ILE A 643 "
            pdb=" C   ILE A 643 "
            pdb=" CB  ILE A 643 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.59   -0.16 2.00e-01 2.50e+01 6.09e-01
  chirality pdb=" CA  VAL B 604 "
            pdb=" N   VAL B 604 "
            pdb=" C   VAL B 604 "
            pdb=" CB  VAL B 604 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.60   -0.15 2.00e-01 2.50e+01 6.00e-01
  ... (remaining 725 not shown)

  Planarity restraints: 739
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE A 637 "    0.030 5.00e-02 4.00e+02   4.62e-02 3.41e+00
        pdb=" N   PRO A 638 "   -0.080 5.00e-02 4.00e+02
        pdb=" CA  PRO A 638 "    0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO A 638 "    0.026 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA B 802 "    0.009 2.00e-02 2.50e+03   1.83e-02 3.36e+00
        pdb=" C   ALA B 802 "   -0.032 2.00e-02 2.50e+03
        pdb=" O   ALA B 802 "    0.012 2.00e-02 2.50e+03
        pdb=" N   ILE B 803 "    0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY B 615 "    0.007 2.00e-02 2.50e+03   1.38e-02 1.91e+00
        pdb=" C   GLY B 615 "   -0.024 2.00e-02 2.50e+03
        pdb=" O   GLY B 615 "    0.009 2.00e-02 2.50e+03
        pdb=" N   LEU B 616 "    0.008 2.00e-02 2.50e+03
  ... (remaining 736 not shown)

  Histogram of nonbonded interaction distances:
        2.35 -     2.86: 1569
        2.86 -     3.37: 4591
        3.37 -     3.88: 7159
        3.88 -     4.39: 7975
        4.39 -     4.90: 13040
  Nonbonded interactions: 34334
  Sorted by model distance:
  nonbonded pdb=" O   SER B 731 "
            pdb=" OG  SER B 734 "
     model   vdw
     2.353 3.040
  nonbonded pdb=" OD1 ASP A 711 "
            pdb=" N   ASP A 712 "
     model   vdw
     2.410 3.120
  nonbonded pdb=" ND2 ASN A 755 "
            pdb=" OE2 GLU A 758 "
     model   vdw
     2.551 3.120
  nonbonded pdb=" O   MET A 682 "
            pdb=" OG1 THR A 686 "
     model   vdw
     2.572 3.040
  nonbonded pdb=" O   LEU A 728 "
            pdb=" OG1 THR A 732 "
     model   vdw
     2.580 3.040
  ... (remaining 34329 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.720
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.060
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     5.100
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.000
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.120
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    7.060
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6633
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   4460  Z= 0.283
  Angle     :  0.742   7.409   6107  Z= 0.463
  Chirality :  0.040   0.214    728
  Planarity :  0.006   0.046    739
  Dihedral  : 11.769  79.357   1539
  Min Nonbonded Distance : 2.353

Molprobity Statistics.
  All-atom Clashscore : 2.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.91 %
    Favored  : 97.09 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.72 %
    Favored  : 97.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.63 (0.35), residues: 549
  helix: -0.12 (0.25), residues: 396
  sheet:  0.13 (1.13), residues: 24
  loop : -1.01 (0.59), residues: 129

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 674 
 TYR   0.013   0.002   TYR A 621 
 PHE   0.013   0.001   PHE B 747 
 TRP   0.011   0.001   TRP B 599 
 HIS   0.004   0.001   HIS B 739 

Details of bonding type rmsd
  covalent geometry    : bond        0.00429 ( 4458)
  covalent geometry    : angle       0.74038 ( 6103)
  SS BOND              : bond        0.00191 (    2)
  SS BOND              : angle       1.91778 (    4)
  hydrogen bonds       : bond        0.15761 (  312)
  hydrogen bonds       : angle       8.06148 (  909)

*********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1098 Ramachandran restraints generated.
    549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1098 Ramachandran restraints generated.
    549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 478 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 163
  time to evaluate  : 0.121 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  603 MET cc_start: 0.3447 (mmm) cc_final: 0.3216 (tpp)
REVERT: A  667 ARG cc_start: 0.5090 (mtt180) cc_final: 0.4099 (ptt90)
REVERT: A  717 ILE cc_start: 0.7628 (mt) cc_final: 0.7411 (mt)
REVERT: A  776 LEU cc_start: 0.8391 (tp) cc_final: 0.8042 (tp)
REVERT: A  793 LEU cc_start: 0.8552 (tp) cc_final: 0.8136 (tp)
REVERT: B  562 ARG cc_start: 0.7141 (mtt-85) cc_final: 0.4155 (mpt180)
REVERT: B  824 TRP cc_start: 0.6411 (m100) cc_final: 0.6141 (t-100)
  outliers start: 0
  outliers final: 0
  residues processed: 163
  average time/residue: 0.0600
  time to fit residues: 12.3295
Evaluate side-chains
  108 residues out of total 478 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 108
  time to evaluate  : 0.094 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 24 optimal weight:    0.9990
   chunk 48 optimal weight:    1.9990
   chunk 26 optimal weight:    0.9980
   chunk 2 optimal weight:    1.9990
   chunk 16 optimal weight:    0.8980
   chunk 32 optimal weight:    0.8980
   chunk 31 optimal weight:    0.7980
   chunk 25 optimal weight:    0.8980
   chunk 50 optimal weight:    0.8980
   chunk 53 optimal weight:    1.9990
   chunk 19 optimal weight:    0.4980
   overall best weight:    0.7980

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 726 ASN
A 731 ASN
B 597 HIS
B 739 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4292 r_free = 0.4292 target = 0.189843 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3953 r_free = 0.3953 target = 0.157600 restraints weight = 5935.595|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.4008 r_free = 0.4008 target = 0.162521 restraints weight = 3436.775|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.4046 r_free = 0.4046 target = 0.165961 restraints weight = 2385.110|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.4067 r_free = 0.4067 target = 0.167994 restraints weight = 1861.916|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.4087 r_free = 0.4087 target = 0.169714 restraints weight = 1584.972|
|-----------------------------------------------------------------------------|
r_work (final): 0.4088
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6711
moved from start:          0.2906

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.065   4460  Z= 0.168
  Angle     :  0.737  10.087   6107  Z= 0.377
  Chirality :  0.045   0.323    728
  Planarity :  0.005   0.055    739
  Dihedral  :  5.909  70.638    593
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 6.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.55 %
    Favored  : 97.45 %
  Rotamer:
    Outliers :  3.35 %
    Allowed  : 11.30 %
    Favored  : 85.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.92 (0.36), residues: 549
  helix:  1.07 (0.26), residues: 403
  sheet: -0.81 (0.87), residues: 37
  loop : -0.30 (0.64), residues: 109

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 707 
 TYR   0.022   0.002   TYR A 621 
 PHE   0.027   0.002   PHE B 777 
 TRP   0.011   0.001   TRP B 716 
 HIS   0.005   0.001   HIS A 562 

Details of bonding type rmsd
  covalent geometry    : bond        0.00378 ( 4458)
  covalent geometry    : angle       0.72592 ( 6103)
  SS BOND              : bond        0.02002 (    2)
  SS BOND              : angle       5.04630 (    4)
  hydrogen bonds       : bond        0.04982 (  312)
  hydrogen bonds       : angle       5.15467 (  909)

*********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1098 Ramachandran restraints generated.
    549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1098 Ramachandran restraints generated.
    549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 478 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 118
  time to evaluate  : 0.168 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  639 LEU cc_start: 0.8504 (OUTLIER) cc_final: 0.8268 (pp)
REVERT: A  669 TYR cc_start: 0.7359 (t80) cc_final: 0.6755 (t80)
REVERT: A  714 LYS cc_start: 0.3214 (mmtt) cc_final: 0.2498 (mmtt)
REVERT: A  793 LEU cc_start: 0.8657 (tp) cc_final: 0.7865 (tp)
REVERT: A  796 THR cc_start: 0.8401 (m) cc_final: 0.8132 (p)
REVERT: A  813 TYR cc_start: 0.6202 (t80) cc_final: 0.5963 (t80)
REVERT: A  821 ARG cc_start: 0.7544 (mtt180) cc_final: 0.7022 (mtp180)
REVERT: B  562 ARG cc_start: 0.6899 (mtt-85) cc_final: 0.4258 (mpt180)
REVERT: B  770 THR cc_start: 0.7637 (m) cc_final: 0.7295 (p)
REVERT: B  820 TYR cc_start: 0.6401 (t80) cc_final: 0.6152 (t80)
  outliers start: 16
  outliers final: 12
  residues processed: 128
  average time/residue: 0.0604
  time to fit residues: 9.8985
Evaluate side-chains
  119 residues out of total 478 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 106
  time to evaluate  : 0.109 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  571 LEU
Chi-restraints excluded: chain A residue  606 LEU
Chi-restraints excluded: chain A residue  620 VAL
Chi-restraints excluded: chain A residue  639 LEU
Chi-restraints excluded: chain A residue  691 VAL
Chi-restraints excluded: chain A residue  754 THR
Chi-restraints excluded: chain A residue  772 SER
Chi-restraints excluded: chain A residue  789 THR
Chi-restraints excluded: chain B residue  650 THR
Chi-restraints excluded: chain B residue  724 LEU
Chi-restraints excluded: chain B residue  781 VAL
Chi-restraints excluded: chain B residue  792 VAL
Chi-restraints excluded: chain B residue  831 GLN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 49 optimal weight:    0.8980
   chunk 43 optimal weight:    2.9990
   chunk 17 optimal weight:    9.9990
   chunk 14 optimal weight:    0.9980
   chunk 41 optimal weight:    0.9980
   chunk 52 optimal weight:    0.8980
   chunk 45 optimal weight:    1.9990
   chunk 11 optimal weight:    0.8980
   chunk 16 optimal weight:    3.9990
   chunk 23 optimal weight:    1.9990
   chunk 33 optimal weight:    0.8980
   overall best weight:    0.9180

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 555 GLN
B 728 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4317 r_free = 0.4317 target = 0.190011 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3991 r_free = 0.3991 target = 0.158338 restraints weight = 5943.932|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4042 r_free = 0.4042 target = 0.163194 restraints weight = 3427.192|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 54)----------------|
| r_work = 0.4078 r_free = 0.4078 target = 0.166571 restraints weight = 2388.139|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.4097 r_free = 0.4097 target = 0.168498 restraints weight = 1856.536|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.4116 r_free = 0.4116 target = 0.170279 restraints weight = 1574.736|
|-----------------------------------------------------------------------------|
r_work (final): 0.4121
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6738
moved from start:          0.3848

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   4460  Z= 0.159
  Angle     :  0.724  14.066   6107  Z= 0.359
  Chirality :  0.043   0.221    728
  Planarity :  0.005   0.060    739
  Dihedral  :  5.657  59.983    593
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 6.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.00 %
    Favored  : 98.00 %
  Rotamer:
    Outliers :  3.56 %
    Allowed  : 14.64 %
    Favored  : 81.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.23 (0.37), residues: 549
  helix:  1.26 (0.26), residues: 405
  sheet: -0.64 (1.03), residues: 27
  loop : -0.12 (0.63), residues: 117

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 707 
 TYR   0.026   0.002   TYR A 724 
 PHE   0.031   0.002   PHE B 622 
 TRP   0.013   0.001   TRP B 716 
 HIS   0.003   0.001   HIS B 597 

Details of bonding type rmsd
  covalent geometry    : bond        0.00360 ( 4458)
  covalent geometry    : angle       0.71762 ( 6103)
  SS BOND              : bond        0.00350 (    2)
  SS BOND              : angle       3.85894 (    4)
  hydrogen bonds       : bond        0.04656 (  312)
  hydrogen bonds       : angle       4.93743 (  909)

*********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1098 Ramachandran restraints generated.
    549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1098 Ramachandran restraints generated.
    549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 478 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 112
  time to evaluate  : 0.109 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  603 MET cc_start: 0.3289 (mmm) cc_final: 0.2862 (ptm)
REVERT: A  647 CYS cc_start: 0.7061 (t) cc_final: 0.6551 (m)
REVERT: A  669 TYR cc_start: 0.7575 (t80) cc_final: 0.6959 (t80)
REVERT: A  682 MET cc_start: 0.5511 (ttm) cc_final: 0.4984 (ttm)
REVERT: A  714 LYS cc_start: 0.3726 (mmtt) cc_final: 0.2891 (mmtt)
REVERT: A  766 MET cc_start: 0.8134 (mmm) cc_final: 0.7533 (mmm)
REVERT: A  793 LEU cc_start: 0.8584 (tp) cc_final: 0.7978 (tp)
REVERT: A  796 THR cc_start: 0.8430 (m) cc_final: 0.8193 (p)
REVERT: A  813 TYR cc_start: 0.6332 (t80) cc_final: 0.6119 (t80)
REVERT: B  562 ARG cc_start: 0.6679 (mtt-85) cc_final: 0.3929 (mpt180)
REVERT: B  565 LYS cc_start: 0.8001 (ttmm) cc_final: 0.7699 (ttmm)
REVERT: B  742 ASN cc_start: 0.7292 (m-40) cc_final: 0.7036 (m110)
REVERT: B  770 THR cc_start: 0.7639 (m) cc_final: 0.7311 (p)
  outliers start: 17
  outliers final: 13
  residues processed: 122
  average time/residue: 0.0505
  time to fit residues: 8.0625
Evaluate side-chains
  117 residues out of total 478 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 104
  time to evaluate  : 0.098 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  571 LEU
Chi-restraints excluded: chain A residue  613 VAL
Chi-restraints excluded: chain A residue  620 VAL
Chi-restraints excluded: chain A residue  691 VAL
Chi-restraints excluded: chain A residue  754 THR
Chi-restraints excluded: chain A residue  772 SER
Chi-restraints excluded: chain A residue  789 THR
Chi-restraints excluded: chain B residue  650 THR
Chi-restraints excluded: chain B residue  724 LEU
Chi-restraints excluded: chain B residue  778 ILE
Chi-restraints excluded: chain B residue  781 VAL
Chi-restraints excluded: chain B residue  792 VAL
Chi-restraints excluded: chain B residue  831 GLN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 8 optimal weight:    0.9980
   chunk 18 optimal weight:    6.9990
   chunk 5 optimal weight:    1.9990
   chunk 3 optimal weight:    0.5980
   chunk 21 optimal weight:    0.7980
   chunk 41 optimal weight:    0.8980
   chunk 4 optimal weight:    1.9990
   chunk 33 optimal weight:    0.9990
   chunk 7 optimal weight:    3.9990
   chunk 46 optimal weight:    0.0970
   chunk 9 optimal weight:    0.9990
   overall best weight:    0.6778

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 555 GLN
A 634 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4366 r_free = 0.4366 target = 0.199884 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.4077 r_free = 0.4077 target = 0.170933 restraints weight = 5582.455|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.4126 r_free = 0.4126 target = 0.175649 restraints weight = 3282.890|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.4162 r_free = 0.4162 target = 0.179013 restraints weight = 2281.088|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.4185 r_free = 0.4185 target = 0.181190 restraints weight = 1764.370|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4197 r_free = 0.4197 target = 0.182553 restraints weight = 1471.072|
|-----------------------------------------------------------------------------|
r_work (final): 0.4200
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6730
moved from start:          0.4245

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   4460  Z= 0.139
  Angle     :  0.698  16.190   6107  Z= 0.342
  Chirality :  0.041   0.210    728
  Planarity :  0.005   0.058    739
  Dihedral  :  5.273  51.752    593
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 6.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.19 %
    Favored  : 97.81 %
  Rotamer:
    Outliers :  4.39 %
    Allowed  : 15.27 %
    Favored  : 80.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.52 (0.37), residues: 549
  helix:  1.42 (0.26), residues: 405
  sheet: -1.05 (1.22), residues: 22
  loop :  0.25 (0.62), residues: 122

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 707 
 TYR   0.022   0.002   TYR A 621 
 PHE   0.021   0.001   PHE B 622 
 TRP   0.014   0.001   TRP B 716 
 HIS   0.002   0.001   HIS B 597 

Details of bonding type rmsd
  covalent geometry    : bond        0.00315 ( 4458)
  covalent geometry    : angle       0.69240 ( 6103)
  SS BOND              : bond        0.00350 (    2)
  SS BOND              : angle       3.37395 (    4)
  hydrogen bonds       : bond        0.04364 (  312)
  hydrogen bonds       : angle       4.76730 (  909)

*********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1098 Ramachandran restraints generated.
    549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1098 Ramachandran restraints generated.
    549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 478 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 109
  time to evaluate  : 0.127 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  585 VAL cc_start: 0.7942 (p) cc_final: 0.7739 (t)
REVERT: A  603 MET cc_start: 0.3284 (mmm) cc_final: 0.2286 (ptm)
REVERT: A  669 TYR cc_start: 0.7338 (t80) cc_final: 0.6799 (t80)
REVERT: A  707 ARG cc_start: 0.6679 (mtm180) cc_final: 0.6226 (mtm180)
REVERT: A  714 LYS cc_start: 0.4057 (mmtt) cc_final: 0.3094 (mmtt)
REVERT: A  766 MET cc_start: 0.8098 (mmm) cc_final: 0.7553 (mmm)
REVERT: A  793 LEU cc_start: 0.8757 (tp) cc_final: 0.8421 (tp)
REVERT: B  565 LYS cc_start: 0.7837 (ttmm) cc_final: 0.7619 (ttmm)
REVERT: B  742 ASN cc_start: 0.7306 (m-40) cc_final: 0.7059 (m110)
REVERT: B  770 THR cc_start: 0.7606 (m) cc_final: 0.7196 (p)
REVERT: B  774 LEU cc_start: 0.8149 (OUTLIER) cc_final: 0.7895 (mp)
  outliers start: 21
  outliers final: 18
  residues processed: 121
  average time/residue: 0.0512
  time to fit residues: 8.0528
Evaluate side-chains
  123 residues out of total 478 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 104
  time to evaluate  : 0.096 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  571 LEU
Chi-restraints excluded: chain A residue  584 LEU
Chi-restraints excluded: chain A residue  613 VAL
Chi-restraints excluded: chain A residue  620 VAL
Chi-restraints excluded: chain A residue  633 ARG
Chi-restraints excluded: chain A residue  691 VAL
Chi-restraints excluded: chain A residue  716 THR
Chi-restraints excluded: chain A residue  754 THR
Chi-restraints excluded: chain A residue  772 SER
Chi-restraints excluded: chain A residue  789 THR
Chi-restraints excluded: chain B residue  650 THR
Chi-restraints excluded: chain B residue  724 LEU
Chi-restraints excluded: chain B residue  755 LEU
Chi-restraints excluded: chain B residue  756 VAL
Chi-restraints excluded: chain B residue  774 LEU
Chi-restraints excluded: chain B residue  778 ILE
Chi-restraints excluded: chain B residue  781 VAL
Chi-restraints excluded: chain B residue  792 VAL
Chi-restraints excluded: chain B residue  831 GLN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 51 optimal weight:    0.6980
   chunk 40 optimal weight:    0.8980
   chunk 37 optimal weight:    3.9990
   chunk 20 optimal weight:    0.7980
   chunk 35 optimal weight:    1.9990
   chunk 15 optimal weight:    8.9990
   chunk 50 optimal weight:    0.9980
   chunk 16 optimal weight:   10.0000
   chunk 10 optimal weight:    4.9990
   chunk 30 optimal weight:    3.9990
   chunk 52 optimal weight:    0.0980
   overall best weight:    0.6980

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 555 GLN
A 723 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4356 r_free = 0.4356 target = 0.198195 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4079 r_free = 0.4079 target = 0.170783 restraints weight = 5804.022|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.4100 r_free = 0.4100 target = 0.173070 restraints weight = 3367.712|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.4104 r_free = 0.4104 target = 0.173576 restraints weight = 2537.009|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4113 r_free = 0.4113 target = 0.174473 restraints weight = 2483.963|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4133 r_free = 0.4133 target = 0.176663 restraints weight = 2120.812|
|-----------------------------------------------------------------------------|
r_work (final): 0.4141
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6734
moved from start:          0.4504

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   4460  Z= 0.147
  Angle     :  0.720  18.217   6107  Z= 0.353
  Chirality :  0.042   0.203    728
  Planarity :  0.005   0.056    739
  Dihedral  :  5.080  44.060    593
  Min Nonbonded Distance : 2.305

Molprobity Statistics.
  All-atom Clashscore : 7.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.37 %
    Favored  : 97.63 %
  Rotamer:
    Outliers :  5.02 %
    Allowed  : 16.95 %
    Favored  : 78.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.49 (0.37), residues: 549
  helix:  1.39 (0.26), residues: 398
  sheet: -0.92 (1.16), residues: 27
  loop :  0.38 (0.62), residues: 124

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 633 
 TYR   0.020   0.001   TYR A 621 
 PHE   0.026   0.001   PHE B 622 
 TRP   0.014   0.001   TRP B 716 
 HIS   0.003   0.001   HIS B 726 

Details of bonding type rmsd
  covalent geometry    : bond        0.00330 ( 4458)
  covalent geometry    : angle       0.71077 ( 6103)
  SS BOND              : bond        0.00374 (    2)
  SS BOND              : angle       4.56538 (    4)
  hydrogen bonds       : bond        0.04318 (  312)
  hydrogen bonds       : angle       4.80974 (  909)

*********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1098 Ramachandran restraints generated.
    549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1098 Ramachandran restraints generated.
    549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 478 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 113
  time to evaluate  : 0.158 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  603 MET cc_start: 0.3058 (mmm) cc_final: 0.2127 (tmm)
REVERT: A  647 CYS cc_start: 0.6618 (t) cc_final: 0.5702 (m)
REVERT: A  654 GLN cc_start: 0.5580 (pt0) cc_final: 0.5320 (tp-100)
REVERT: A  669 TYR cc_start: 0.7586 (t80) cc_final: 0.7023 (t80)
REVERT: A  697 MET cc_start: 0.6019 (tpp) cc_final: 0.5740 (ttp)
REVERT: A  707 ARG cc_start: 0.7052 (mtm180) cc_final: 0.6187 (mtm180)
REVERT: A  714 LYS cc_start: 0.3943 (mmtt) cc_final: 0.2784 (mmtt)
REVERT: A  766 MET cc_start: 0.8150 (mmm) cc_final: 0.7597 (mmm)
REVERT: B  565 LYS cc_start: 0.8194 (ttmm) cc_final: 0.7957 (ttmm)
REVERT: B  770 THR cc_start: 0.7603 (m) cc_final: 0.7107 (p)
REVERT: B  774 LEU cc_start: 0.8035 (OUTLIER) cc_final: 0.7787 (mp)
  outliers start: 24
  outliers final: 20
  residues processed: 125
  average time/residue: 0.0512
  time to fit residues: 8.4438
Evaluate side-chains
  128 residues out of total 478 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 107
  time to evaluate  : 0.153 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  571 LEU
Chi-restraints excluded: chain A residue  584 LEU
Chi-restraints excluded: chain A residue  613 VAL
Chi-restraints excluded: chain A residue  620 VAL
Chi-restraints excluded: chain A residue  631 LEU
Chi-restraints excluded: chain A residue  633 ARG
Chi-restraints excluded: chain A residue  691 VAL
Chi-restraints excluded: chain A residue  716 THR
Chi-restraints excluded: chain A residue  754 THR
Chi-restraints excluded: chain A residue  772 SER
Chi-restraints excluded: chain A residue  780 MET
Chi-restraints excluded: chain A residue  789 THR
Chi-restraints excluded: chain B residue  567 LEU
Chi-restraints excluded: chain B residue  650 THR
Chi-restraints excluded: chain B residue  724 LEU
Chi-restraints excluded: chain B residue  755 LEU
Chi-restraints excluded: chain B residue  756 VAL
Chi-restraints excluded: chain B residue  774 LEU
Chi-restraints excluded: chain B residue  781 VAL
Chi-restraints excluded: chain B residue  792 VAL
Chi-restraints excluded: chain B residue  831 GLN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 42 optimal weight:    2.9990
   chunk 36 optimal weight:    0.8980
   chunk 3 optimal weight:    0.9980
   chunk 8 optimal weight:    0.8980
   chunk 18 optimal weight:    8.9990
   chunk 48 optimal weight:    0.7980
   chunk 39 optimal weight:    1.9990
   chunk 30 optimal weight:    3.9990
   chunk 47 optimal weight:    0.7980
   chunk 0 optimal weight:    5.9990
   chunk 50 optimal weight:    0.0980
   overall best weight:    0.6980

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 723 ASN
B 742 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4329 r_free = 0.4329 target = 0.191726 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3996 r_free = 0.3996 target = 0.159766 restraints weight = 6128.565|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4050 r_free = 0.4050 target = 0.164693 restraints weight = 3438.862|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.4085 r_free = 0.4085 target = 0.168053 restraints weight = 2371.346|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.4107 r_free = 0.4107 target = 0.170333 restraints weight = 1843.953|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.4130 r_free = 0.4130 target = 0.172136 restraints weight = 1551.500|
|-----------------------------------------------------------------------------|
r_work (final): 0.4135
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6692
moved from start:          0.4773

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   4460  Z= 0.143
  Angle     :  0.711  17.898   6107  Z= 0.344
  Chirality :  0.043   0.201    728
  Planarity :  0.005   0.051    739
  Dihedral  :  4.896  35.520    593
  Min Nonbonded Distance : 2.334

Molprobity Statistics.
  All-atom Clashscore : 8.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.00 %
    Favored  : 98.00 %
  Rotamer:
    Outliers :  5.44 %
    Allowed  : 17.36 %
    Favored  : 77.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.44 (0.37), residues: 549
  helix:  1.42 (0.26), residues: 396
  sheet: -1.70 (1.23), residues: 20
  loop :  0.21 (0.59), residues: 133

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 633 
 TYR   0.023   0.001   TYR A 621 
 PHE   0.024   0.001   PHE B 622 
 TRP   0.016   0.001   TRP B 716 
 HIS   0.004   0.001   HIS B 728 

Details of bonding type rmsd
  covalent geometry    : bond        0.00326 ( 4458)
  covalent geometry    : angle       0.70535 ( 6103)
  SS BOND              : bond        0.00470 (    2)
  SS BOND              : angle       3.66986 (    4)
  hydrogen bonds       : bond        0.04212 (  312)
  hydrogen bonds       : angle       4.88682 (  909)

*********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1098 Ramachandran restraints generated.
    549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1098 Ramachandran restraints generated.
    549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 478 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 114
  time to evaluate  : 0.165 
Fit side-chains
   revert: symmetry clash
REVERT: A  603 MET cc_start: 0.3224 (mmm) cc_final: 0.2171 (tmm)
REVERT: A  607 MET cc_start: 0.6250 (ttm) cc_final: 0.5946 (mtt)
REVERT: A  647 CYS cc_start: 0.6231 (t) cc_final: 0.5519 (m)
REVERT: A  654 GLN cc_start: 0.5764 (pt0) cc_final: 0.5533 (tp-100)
REVERT: A  669 TYR cc_start: 0.7553 (t80) cc_final: 0.7003 (t80)
REVERT: A  707 ARG cc_start: 0.7034 (OUTLIER) cc_final: 0.6397 (mtm180)
REVERT: A  714 LYS cc_start: 0.3940 (mmtt) cc_final: 0.2806 (mmtt)
REVERT: A  766 MET cc_start: 0.8078 (mmm) cc_final: 0.7534 (mmm)
REVERT: A  793 LEU cc_start: 0.8246 (tp) cc_final: 0.7740 (tp)
REVERT: B  770 THR cc_start: 0.7606 (m) cc_final: 0.7349 (p)
REVERT: B  774 LEU cc_start: 0.8206 (OUTLIER) cc_final: 0.7721 (tp)
  outliers start: 26
  outliers final: 19
  residues processed: 129
  average time/residue: 0.0473
  time to fit residues: 8.0638
Evaluate side-chains
  125 residues out of total 478 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 104
  time to evaluate  : 0.094 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  571 LEU
Chi-restraints excluded: chain A residue  584 LEU
Chi-restraints excluded: chain A residue  613 VAL
Chi-restraints excluded: chain A residue  620 VAL
Chi-restraints excluded: chain A residue  631 LEU
Chi-restraints excluded: chain A residue  655 ILE
Chi-restraints excluded: chain A residue  691 VAL
Chi-restraints excluded: chain A residue  707 ARG
Chi-restraints excluded: chain A residue  716 THR
Chi-restraints excluded: chain A residue  754 THR
Chi-restraints excluded: chain A residue  772 SER
Chi-restraints excluded: chain A residue  780 MET
Chi-restraints excluded: chain A residue  789 THR
Chi-restraints excluded: chain B residue  650 THR
Chi-restraints excluded: chain B residue  724 LEU
Chi-restraints excluded: chain B residue  755 LEU
Chi-restraints excluded: chain B residue  756 VAL
Chi-restraints excluded: chain B residue  774 LEU
Chi-restraints excluded: chain B residue  781 VAL
Chi-restraints excluded: chain B residue  792 VAL
Chi-restraints excluded: chain B residue  831 GLN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 9 optimal weight:    1.9990
   chunk 33 optimal weight:    0.7980
   chunk 20 optimal weight:    0.8980
   chunk 13 optimal weight:    0.9990
   chunk 1 optimal weight:    2.9990
   chunk 8 optimal weight:    0.9990
   chunk 14 optimal weight:    4.9990
   chunk 53 optimal weight:    0.0270
   chunk 21 optimal weight:    0.9980
   chunk 19 optimal weight:    3.9990
   chunk 18 optimal weight:    0.6980
   overall best weight:    0.6838

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 723 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4334 r_free = 0.4334 target = 0.193187 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4012 r_free = 0.4012 target = 0.160980 restraints weight = 5939.360|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4061 r_free = 0.4061 target = 0.165810 restraints weight = 3441.604|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.4097 r_free = 0.4097 target = 0.169147 restraints weight = 2392.934|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4116 r_free = 0.4116 target = 0.171214 restraints weight = 1866.188|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.4140 r_free = 0.4140 target = 0.173235 restraints weight = 1576.751|
|-----------------------------------------------------------------------------|
r_work (final): 0.4140
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6695
moved from start:          0.4979

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   4460  Z= 0.143
  Angle     :  0.722  18.129   6107  Z= 0.351
  Chirality :  0.042   0.205    728
  Planarity :  0.005   0.048    739
  Dihedral  :  4.687  23.264    593
  Min Nonbonded Distance : 2.344

Molprobity Statistics.
  All-atom Clashscore : 7.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.00 %
    Favored  : 98.00 %
  Rotamer:
    Outliers :  5.23 %
    Allowed  : 18.20 %
    Favored  : 76.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.48 (0.37), residues: 549
  helix:  1.44 (0.26), residues: 397
  sheet: -1.87 (1.17), residues: 22
  loop :  0.31 (0.60), residues: 130

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 633 
 TYR   0.040   0.002   TYR A 621 
 PHE   0.032   0.001   PHE B 622 
 TRP   0.015   0.001   TRP B 716 
 HIS   0.002   0.001   HIS B 646 

Details of bonding type rmsd
  covalent geometry    : bond        0.00333 ( 4458)
  covalent geometry    : angle       0.71708 ( 6103)
  SS BOND              : bond        0.00114 (    2)
  SS BOND              : angle       3.26733 (    4)
  hydrogen bonds       : bond        0.04129 (  312)
  hydrogen bonds       : angle       4.83280 (  909)

*********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1098 Ramachandran restraints generated.
    549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1098 Ramachandran restraints generated.
    549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 478 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 111
  time to evaluate  : 0.163 
Fit side-chains
   revert: symmetry clash
REVERT: A  603 MET cc_start: 0.3167 (mmm) cc_final: 0.2019 (tmm)
REVERT: A  669 TYR cc_start: 0.7592 (t80) cc_final: 0.7054 (t80)
REVERT: A  707 ARG cc_start: 0.7030 (OUTLIER) cc_final: 0.6415 (mtm180)
REVERT: A  714 LYS cc_start: 0.3920 (mmtt) cc_final: 0.2798 (mmtt)
REVERT: A  766 MET cc_start: 0.8060 (mmm) cc_final: 0.7545 (mmm)
REVERT: B  804 LEU cc_start: 0.8533 (mt) cc_final: 0.8283 (mt)
REVERT: B  831 GLN cc_start: 0.7935 (OUTLIER) cc_final: 0.7653 (tm-30)
  outliers start: 25
  outliers final: 20
  residues processed: 123
  average time/residue: 0.0611
  time to fit residues: 9.8952
Evaluate side-chains
  123 residues out of total 478 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 101
  time to evaluate  : 0.159 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  571 LEU
Chi-restraints excluded: chain A residue  584 LEU
Chi-restraints excluded: chain A residue  613 VAL
Chi-restraints excluded: chain A residue  620 VAL
Chi-restraints excluded: chain A residue  631 LEU
Chi-restraints excluded: chain A residue  655 ILE
Chi-restraints excluded: chain A residue  691 VAL
Chi-restraints excluded: chain A residue  707 ARG
Chi-restraints excluded: chain A residue  716 THR
Chi-restraints excluded: chain A residue  754 THR
Chi-restraints excluded: chain A residue  772 SER
Chi-restraints excluded: chain A residue  780 MET
Chi-restraints excluded: chain A residue  789 THR
Chi-restraints excluded: chain B residue  650 THR
Chi-restraints excluded: chain B residue  724 LEU
Chi-restraints excluded: chain B residue  755 LEU
Chi-restraints excluded: chain B residue  756 VAL
Chi-restraints excluded: chain B residue  778 ILE
Chi-restraints excluded: chain B residue  781 VAL
Chi-restraints excluded: chain B residue  792 VAL
Chi-restraints excluded: chain B residue  803 ILE
Chi-restraints excluded: chain B residue  831 GLN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 21 optimal weight:    0.6980
   chunk 37 optimal weight:    2.9990
   chunk 3 optimal weight:    2.9990
   chunk 53 optimal weight:    0.0770
   chunk 39 optimal weight:    2.9990
   chunk 10 optimal weight:    7.9990
   chunk 17 optimal weight:    8.9990
   chunk 34 optimal weight:    0.9990
   chunk 33 optimal weight:    0.9980
   chunk 0 optimal weight:    5.9990
   chunk 49 optimal weight:    1.9990
   overall best weight:    0.9542

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 654 GLN
A 723 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4317 r_free = 0.4317 target = 0.191868 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3993 r_free = 0.3993 target = 0.159383 restraints weight = 5875.540|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4042 r_free = 0.4042 target = 0.164162 restraints weight = 3438.485|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.4078 r_free = 0.4078 target = 0.167499 restraints weight = 2385.061|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.4098 r_free = 0.4098 target = 0.169580 restraints weight = 1860.943|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.4117 r_free = 0.4117 target = 0.171328 restraints weight = 1574.751|
|-----------------------------------------------------------------------------|
r_work (final): 0.4117
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6730
moved from start:          0.5160

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   4460  Z= 0.161
  Angle     :  0.757  17.795   6107  Z= 0.366
  Chirality :  0.043   0.221    728
  Planarity :  0.005   0.048    739
  Dihedral  :  4.760  22.950    593
  Min Nonbonded Distance : 2.351

Molprobity Statistics.
  All-atom Clashscore : 7.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.37 %
    Favored  : 97.63 %
  Rotamer:
    Outliers :  5.65 %
    Allowed  : 18.83 %
    Favored  : 75.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.43 (0.37), residues: 549
  helix:  1.40 (0.26), residues: 396
  sheet: -2.12 (1.19), residues: 22
  loop :  0.38 (0.59), residues: 131

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 707 
 TYR   0.050   0.002   TYR A 621 
 PHE   0.029   0.002   PHE B 622 
 TRP   0.017   0.001   TRP B 716 
 HIS   0.002   0.001   HIS B 646 

Details of bonding type rmsd
  covalent geometry    : bond        0.00378 ( 4458)
  covalent geometry    : angle       0.75228 ( 6103)
  SS BOND              : bond        0.00314 (    2)
  SS BOND              : angle       3.25523 (    4)
  hydrogen bonds       : bond        0.04324 (  312)
  hydrogen bonds       : angle       4.87316 (  909)

*********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1098 Ramachandran restraints generated.
    549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1098 Ramachandran restraints generated.
    549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 478 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 110
  time to evaluate  : 0.187 
Fit side-chains
   revert: symmetry clash
REVERT: A  560 GLU cc_start: 0.6778 (tp30) cc_final: 0.6257 (mt-10)
REVERT: A  603 MET cc_start: 0.3438 (mmm) cc_final: 0.2216 (tmm)
REVERT: A  669 TYR cc_start: 0.7654 (t80) cc_final: 0.7115 (t80)
REVERT: A  714 LYS cc_start: 0.3946 (mmtt) cc_final: 0.2803 (mmtt)
REVERT: A  748 MET cc_start: 0.6662 (mmm) cc_final: 0.6355 (mmm)
REVERT: A  766 MET cc_start: 0.8064 (mmm) cc_final: 0.7516 (mmm)
REVERT: A  793 LEU cc_start: 0.8505 (tp) cc_final: 0.7897 (tp)
REVERT: B  804 LEU cc_start: 0.8586 (mt) cc_final: 0.8325 (mt)
REVERT: B  831 GLN cc_start: 0.8010 (OUTLIER) cc_final: 0.7753 (tm-30)
  outliers start: 27
  outliers final: 22
  residues processed: 125
  average time/residue: 0.0565
  time to fit residues: 9.3332
Evaluate side-chains
  127 residues out of total 478 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 104
  time to evaluate  : 0.166 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  571 LEU
Chi-restraints excluded: chain A residue  584 LEU
Chi-restraints excluded: chain A residue  613 VAL
Chi-restraints excluded: chain A residue  620 VAL
Chi-restraints excluded: chain A residue  631 LEU
Chi-restraints excluded: chain A residue  655 ILE
Chi-restraints excluded: chain A residue  691 VAL
Chi-restraints excluded: chain A residue  716 THR
Chi-restraints excluded: chain A residue  723 ASN
Chi-restraints excluded: chain A residue  754 THR
Chi-restraints excluded: chain A residue  772 SER
Chi-restraints excluded: chain A residue  780 MET
Chi-restraints excluded: chain A residue  789 THR
Chi-restraints excluded: chain B residue  650 THR
Chi-restraints excluded: chain B residue  724 LEU
Chi-restraints excluded: chain B residue  728 HIS
Chi-restraints excluded: chain B residue  755 LEU
Chi-restraints excluded: chain B residue  756 VAL
Chi-restraints excluded: chain B residue  778 ILE
Chi-restraints excluded: chain B residue  781 VAL
Chi-restraints excluded: chain B residue  792 VAL
Chi-restraints excluded: chain B residue  803 ILE
Chi-restraints excluded: chain B residue  831 GLN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 33 optimal weight:    0.8980
   chunk 28 optimal weight:    0.9990
   chunk 9 optimal weight:    1.9990
   chunk 37 optimal weight:    3.9990
   chunk 47 optimal weight:    0.7980
   chunk 44 optimal weight:    0.4980
   chunk 12 optimal weight:    2.9990
   chunk 19 optimal weight:    2.9990
   chunk 45 optimal weight:    0.6980
   chunk 21 optimal weight:    0.6980
   chunk 10 optimal weight:    5.9990
   overall best weight:    0.7180

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 654 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4324 r_free = 0.4324 target = 0.192640 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3999 r_free = 0.3999 target = 0.159863 restraints weight = 5999.472|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.4050 r_free = 0.4050 target = 0.164795 restraints weight = 3497.464|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4076 r_free = 0.4076 target = 0.167645 restraints weight = 2419.407|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.4107 r_free = 0.4107 target = 0.170269 restraints weight = 1914.602|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.4119 r_free = 0.4119 target = 0.171639 restraints weight = 1602.825|
|-----------------------------------------------------------------------------|
r_work (final): 0.4122
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6730
moved from start:          0.5273

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   4460  Z= 0.148
  Angle     :  0.757  16.981   6107  Z= 0.366
  Chirality :  0.043   0.218    728
  Planarity :  0.005   0.045    739
  Dihedral  :  4.734  22.369    593
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 6.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.19 %
    Favored  : 97.81 %
  Rotamer:
    Outliers :  5.02 %
    Allowed  : 19.67 %
    Favored  : 75.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.42 (0.37), residues: 549
  helix:  1.45 (0.26), residues: 396
  sheet: -1.92 (1.27), residues: 20
  loop :  0.09 (0.58), residues: 133

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 707 
 TYR   0.050   0.002   TYR A 621 
 PHE   0.038   0.002   PHE B 622 
 TRP   0.016   0.001   TRP B 716 
 HIS   0.002   0.001   HIS B 646 

Details of bonding type rmsd
  covalent geometry    : bond        0.00345 ( 4458)
  covalent geometry    : angle       0.75356 ( 6103)
  SS BOND              : bond        0.00282 (    2)
  SS BOND              : angle       2.93826 (    4)
  hydrogen bonds       : bond        0.04251 (  312)
  hydrogen bonds       : angle       4.81420 (  909)

*********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1098 Ramachandran restraints generated.
    549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1098 Ramachandran restraints generated.
    549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 478 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 104
  time to evaluate  : 0.159 
Fit side-chains
   revert: symmetry clash
REVERT: A  560 GLU cc_start: 0.6855 (tp30) cc_final: 0.6486 (mt-10)
REVERT: A  603 MET cc_start: 0.3420 (mmm) cc_final: 0.2215 (tmm)
REVERT: A  669 TYR cc_start: 0.7657 (t80) cc_final: 0.7048 (t80)
REVERT: A  707 ARG cc_start: 0.6952 (OUTLIER) cc_final: 0.6587 (ptm-80)
REVERT: A  714 LYS cc_start: 0.3667 (mmtt) cc_final: 0.2430 (mmtt)
REVERT: A  748 MET cc_start: 0.6706 (mmm) cc_final: 0.6323 (mmm)
REVERT: A  766 MET cc_start: 0.8002 (mmm) cc_final: 0.7514 (mmm)
REVERT: A  793 LEU cc_start: 0.8510 (tp) cc_final: 0.7899 (tp)
REVERT: B  831 GLN cc_start: 0.7980 (OUTLIER) cc_final: 0.7748 (tm-30)
  outliers start: 24
  outliers final: 22
  residues processed: 119
  average time/residue: 0.0524
  time to fit residues: 8.3798
Evaluate side-chains
  128 residues out of total 478 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 104
  time to evaluate  : 0.155 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  571 LEU
Chi-restraints excluded: chain A residue  584 LEU
Chi-restraints excluded: chain A residue  613 VAL
Chi-restraints excluded: chain A residue  620 VAL
Chi-restraints excluded: chain A residue  631 LEU
Chi-restraints excluded: chain A residue  691 VAL
Chi-restraints excluded: chain A residue  707 ARG
Chi-restraints excluded: chain A residue  716 THR
Chi-restraints excluded: chain A residue  754 THR
Chi-restraints excluded: chain A residue  772 SER
Chi-restraints excluded: chain A residue  780 MET
Chi-restraints excluded: chain A residue  789 THR
Chi-restraints excluded: chain B residue  650 THR
Chi-restraints excluded: chain B residue  714 THR
Chi-restraints excluded: chain B residue  724 LEU
Chi-restraints excluded: chain B residue  728 HIS
Chi-restraints excluded: chain B residue  755 LEU
Chi-restraints excluded: chain B residue  756 VAL
Chi-restraints excluded: chain B residue  774 LEU
Chi-restraints excluded: chain B residue  778 ILE
Chi-restraints excluded: chain B residue  781 VAL
Chi-restraints excluded: chain B residue  792 VAL
Chi-restraints excluded: chain B residue  803 ILE
Chi-restraints excluded: chain B residue  831 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 0 optimal weight:    5.9990
   chunk 30 optimal weight:    0.0030
   chunk 33 optimal weight:    0.7980
   chunk 27 optimal weight:    1.9990
   chunk 39 optimal weight:    1.9990
   chunk 28 optimal weight:    0.6980
   chunk 14 optimal weight:    5.9990
   chunk 13 optimal weight:    2.9990
   chunk 45 optimal weight:    1.9990
   chunk 29 optimal weight:    0.8980
   chunk 20 optimal weight:    0.7980
   overall best weight:    0.6390

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4331 r_free = 0.4331 target = 0.193549 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4009 r_free = 0.4009 target = 0.161324 restraints weight = 5903.335|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.4060 r_free = 0.4060 target = 0.166224 restraints weight = 3395.332|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4088 r_free = 0.4088 target = 0.169217 restraints weight = 2334.599|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.4119 r_free = 0.4119 target = 0.171796 restraints weight = 1828.394|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4132 r_free = 0.4132 target = 0.173183 restraints weight = 1524.161|
|-----------------------------------------------------------------------------|
r_work (final): 0.4136
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6696
moved from start:          0.5404

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   4460  Z= 0.140
  Angle     :  0.763  17.370   6107  Z= 0.365
  Chirality :  0.042   0.214    728
  Planarity :  0.005   0.045    739
  Dihedral  :  4.654  21.950    593
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 7.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.82 %
    Favored  : 98.18 %
  Rotamer:
    Outliers :  5.02 %
    Allowed  : 19.87 %
    Favored  : 75.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.42 (0.37), residues: 549
  helix:  1.48 (0.26), residues: 397
  sheet: -2.03 (1.26), residues: 20
  loop :  0.00 (0.58), residues: 132

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 707 
 TYR   0.046   0.002   TYR A 621 
 PHE   0.037   0.002   PHE B 622 
 TRP   0.017   0.001   TRP B 716 
 HIS   0.002   0.001   HIS B 815 

Details of bonding type rmsd
  covalent geometry    : bond        0.00324 ( 4458)
  covalent geometry    : angle       0.76022 ( 6103)
  SS BOND              : bond        0.00296 (    2)
  SS BOND              : angle       2.77247 (    4)
  hydrogen bonds       : bond        0.04209 (  312)
  hydrogen bonds       : angle       4.72036 (  909)

********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1098 Ramachandran restraints generated.
    549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1098 Ramachandran restraints generated.
    549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 478 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 106
  time to evaluate  : 0.158 
Fit side-chains
   revert: symmetry clash
REVERT: A  669 TYR cc_start: 0.7462 (t80) cc_final: 0.6982 (t80)
REVERT: A  707 ARG cc_start: 0.7222 (OUTLIER) cc_final: 0.6917 (ptm-80)
REVERT: A  714 LYS cc_start: 0.3966 (mmtt) cc_final: 0.2825 (mmtt)
REVERT: A  748 MET cc_start: 0.6760 (mmm) cc_final: 0.6453 (mmm)
REVERT: A  766 MET cc_start: 0.7870 (mmm) cc_final: 0.7333 (mmm)
REVERT: A  793 LEU cc_start: 0.8723 (tp) cc_final: 0.8047 (tp)
REVERT: B  831 GLN cc_start: 0.7981 (OUTLIER) cc_final: 0.7737 (tm-30)
  outliers start: 24
  outliers final: 20
  residues processed: 119
  average time/residue: 0.0561
  time to fit residues: 8.9722
Evaluate side-chains
  126 residues out of total 478 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 104
  time to evaluate  : 0.096 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  571 LEU
Chi-restraints excluded: chain A residue  584 LEU
Chi-restraints excluded: chain A residue  613 VAL
Chi-restraints excluded: chain A residue  620 VAL
Chi-restraints excluded: chain A residue  631 LEU
Chi-restraints excluded: chain A residue  691 VAL
Chi-restraints excluded: chain A residue  707 ARG
Chi-restraints excluded: chain A residue  716 THR
Chi-restraints excluded: chain A residue  754 THR
Chi-restraints excluded: chain A residue  772 SER
Chi-restraints excluded: chain A residue  780 MET
Chi-restraints excluded: chain A residue  789 THR
Chi-restraints excluded: chain B residue  650 THR
Chi-restraints excluded: chain B residue  724 LEU
Chi-restraints excluded: chain B residue  755 LEU
Chi-restraints excluded: chain B residue  756 VAL
Chi-restraints excluded: chain B residue  774 LEU
Chi-restraints excluded: chain B residue  778 ILE
Chi-restraints excluded: chain B residue  781 VAL
Chi-restraints excluded: chain B residue  792 VAL
Chi-restraints excluded: chain B residue  803 ILE
Chi-restraints excluded: chain B residue  831 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 18 optimal weight:    8.9990
   chunk 1 optimal weight:    0.9990
   chunk 16 optimal weight:    0.4980
   chunk 9 optimal weight:    1.9990
   chunk 17 optimal weight:    1.9990
   chunk 52 optimal weight:    0.3980
   chunk 3 optimal weight:    1.9990
   chunk 32 optimal weight:    0.7980
   chunk 47 optimal weight:    0.3980
   chunk 39 optimal weight:    1.9990
   chunk 15 optimal weight:    0.7980
   overall best weight:    0.5780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4331 r_free = 0.4331 target = 0.193518 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4009 r_free = 0.4009 target = 0.161211 restraints weight = 5963.241|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.4058 r_free = 0.4058 target = 0.166021 restraints weight = 3400.943|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.4093 r_free = 0.4093 target = 0.169357 restraints weight = 2343.601|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4113 r_free = 0.4113 target = 0.171389 restraints weight = 1813.615|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.4129 r_free = 0.4129 target = 0.172945 restraints weight = 1525.950|
|-----------------------------------------------------------------------------|
r_work (final): 0.4133
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6692
moved from start:          0.5497

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   4460  Z= 0.139
  Angle     :  0.763  17.105   6107  Z= 0.363
  Chirality :  0.042   0.215    728
  Planarity :  0.005   0.045    739
  Dihedral  :  4.583  21.268    593
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 6.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.46 %
    Favored  : 98.54 %
  Rotamer:
    Outliers :  5.44 %
    Allowed  : 20.50 %
    Favored  : 74.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.46 (0.37), residues: 549
  helix:  1.53 (0.26), residues: 397
  sheet: -1.97 (1.27), residues: 20
  loop : -0.12 (0.57), residues: 132

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 707 
 TYR   0.039   0.001   TYR A 621 
 PHE   0.038   0.002   PHE B 622 
 TRP   0.015   0.001   TRP B 716 
 HIS   0.002   0.001   HIS B 815 

Details of bonding type rmsd
  covalent geometry    : bond        0.00319 ( 4458)
  covalent geometry    : angle       0.75991 ( 6103)
  SS BOND              : bond        0.00295 (    2)
  SS BOND              : angle       2.72285 (    4)
  hydrogen bonds       : bond        0.04091 (  312)
  hydrogen bonds       : angle       4.74784 (  909)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 783.63 seconds
wall clock time: 14 minutes 9.10 seconds (849.10 seconds total)